[Gmod-help] GBROWSE Question

[Victor Gordo Bayarri]

Hello,

I have a question regarding Gbrowse, I've read the wiki and 
documentation but I don't find what is wrong in my implementation.

I try to group genes in one track with the Name attribute in the GFF3 
file, and it seems to work, but there are some genes that appear 
separate from the others even though they have the same Name attribute.

My Gff3 file has the following structure for example:

contig00791     analisi contig  1       16959   .       .       .       
Name=contig00791
contig00791     analisi blastn  15985   16057   73      -       .       
ID=FBgn0003138contig00791blastn;Name=Ptp61F;Summary=...;FBgn=FBgn0003138;GenInici=45046;GenFinal=44974;
contig00791     analisi blastn  15985   16057   73      -       .       
ID=FBgn0003138contig00791blastn;Name=Ptp61F;Summary=...;FBgn=FBgn0003138;GenInici=44742;GenFinal=44670;
contig00791     analisi blastn  15985   16057   73      -       .       
ID=FBgn0003138contig00791blastn;Name=Ptp61F;Summary=...;FBgn=FBgn0003138;GenInici=44451;GenFinal=44379;
contig00791     analisi blastn  15985   16057   73      -       .       
ID=FBgn0003138contig00791blastn;Name=Ptp61F;Summary=...;FBgn=FBgn0003138;GenInici=26574;GenFinal=26502;
contig00791     analisi blastn  15985   16057   73      -       .       
ID=FBgn0003138contig00791blastn;Name=Ptp61F;Summary=...;FBgn=FBgn0003138;GenInici=23540;GenFinal=23468;
contig00791     analisi blastn  15985   16057   73      -       .       
ID=FBgn0003138contig00791blastn;Name=Ptp61F;Summary=...;FBgn=FBgn0003138;GenInici=23199;GenFinal=23127;
contig00791     analisi blastn  15985   16056   72      -       .       
ID=FBgn0003138contig00791blastn;Name=Ptp61F;Summary=...;FBgn=FBgn0003138;GenInici=27285;GenFinal=27214;
contig00791     analisi blastn  15985   16056   72      -       .       
ID=FBgn0003138contig00791blastn;Name=Ptp61F;Summary=...;FBgn=FBgn0003138;GenInici=27048;GenFinal=26977;
contig00791     analisi blastn  15985   16056   72      -       .       
ID=FBgn0003138contig00791blastn;Name=Ptp61F;Summary=...;FBgn=FBgn0003138;GenInici=26811;GenFinal=26740;
contig00791     analisi blastn  16874   16952   55      +       .       
ID=FBgn0003138contig00791blastn;Name=Ptp61F;Summary=...;FBgn=FBgn0003138;GenInici=44971;GenFinal=45049;
contig00791     analisi blastn  15550   15627   54      +       .       
ID=FBgn0003138contig00791blastn;Name=Ptp61F;Summary=...;FBgn=FBgn0003138;GenInici=44971;GenFinal=45048;
contig00791     analisi blastn  16876   16952   53      +       .       
ID=FBgn0003138contig00791blastn;Name=Ptp61F;Summary=...;FBgn=FBgn0003138;GenInici=26501;GenFinal=26577;
contig00791     analisi blastn  15550   15625   52      +       .       
ID=FBgn0003138contig00791blastn;Name=Ptp61F;Summary=...;FBgn=FBgn0003138;GenInici=44376;GenFinal=44451;
contig00791     analisi blastn  15550   15625   52      +       .       
ID=FBgn0003138contig00791blastn;Name=Ptp61F;Summary=...;FBgn=FBgn0003138;GenInici=44667;GenFinal=44742;
contig00791     analisi blastn  15552   15627   52      +       .       
ID=FBgn0003138contig00791blastn;Name=Ptp61F;Summary=...;FBgn=FBgn0003138;GenInici=26501;GenFinal=26576;
...
...
...

I send you some example images:
GBROWSE.jpg: you can see the "Ptp61F" gene grouped above and some genes 
not grouped below (why?).
GBROWSE2.jpg: here is the information that appears when you click the 
grouped genes.
GBROWSE3.jpg: here is the information that appears when you click for 
example one of the not grouped genes.

Can you help me to find whay sometimes the genes appear grouped and 
sometimes not?

Thank you for your help,

Victor.

-- 
--
------------------------------------------

Victor Gordo Bayarri
Unitat de Bioinformàtica
Serveis Cientificotècnics - Universitat de Barcelona
Edifici Modular-Parc Científic de Barcelona
c/ Baldiri Reixac, nº 10-12
08028 Barcelona

Email: vgordo at sct.ub.es
Tel: +34 934020455

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